VIJAY SHANKAR CURRICULUM VITAE DR. VIJAY SHANKAR, PH. D.

CURRENT POSITION Bioinformatics Staff Scientist Center for Human Genetics of Clemson

ADDRESS 152 Self Regional Hall 114 Gregor Mendel Cir, Greenwood, SC 29646 tel. (1) 216-410-0846 e-mail: [email protected]

EDUCATION

Ph.D. Wright State University, Dayton, OH, USA 2010-2016 Biomedical

Bachelor of Arts (BA) Miami University, Oxford, OH, USA 2004-2008 Microbiology

POSITIONS

Bioinformatics Staff Scientist Clemson University, Greenwood, SC 2019-Present

Bioinformatics Research Associate Clemson University, Clemson, SC 2016-2018

Research Assistant Wright State University, Dayton, OH 2016

GRANTS, HONORS AND AWARDS Center for Produce Safety Grant Award: 2019CPS07 – Co-PI with Dr. Jiang and Dr. Saski 2018 Best student poster presentation at Ohio Branch American Society of Microbiology 2014 Recipient of the Original Works Grant from Wright State Graduate Student Assembly 2012 Graduate Teaching Assistantship at Wright State University 2009 – 2010 Ohio Leaders Scholarship at Miami University 2004 – 2008 National Scholarship Survey Recognition 2004 – 2008 Dean’s List at Miami University 2007 Robotics and Mechanics Award for High School Seniors from Cuyohoga Community College 2003

MEMBERSHIPS

American Society for Microbiology 2012 – present

VIJAY SHANKAR CURRICULUM VITAE

AREAS OF RESEARCH INTERESTS

Development and application of multivariate statistics in a wide array of subjects and fields Development of new pipelines and improvement of current ones for analysis of NGS data Role of intestinal microbiota in human health and disease Metabolic interactions in complex microbial communities

PUBLICATIONS

• R. E. Noorai, V. Shankar*, N. H. Freese, C. M. Gregorski and S. C. Chapman. (2019) Discovery of genomic variants by whole-genome requencing of the North American Araucana chicken. PLOS ONE 14(12): e0225834. PMC6903725 *co-first author – equal contribution with R. E. Noorai. • D. Nayduch, V. Shankar, M. K. Mills, T. Robl, B. Drolet, M. Ruder, E. Scully and C. Saski. (2019) Transcriptome response of female Culicoides sonorensis biting midges (Diptera: Ceratopogonidae) to early infection with Epizootic Hemorrhagic Disease Virus (EHDV-2). Viruses 11(5): 473. PMC6563219 • S. K. Krombeen, V. Shankar, R. E. Noorai, C. Saski, J. Sharp, M. Wilson and T. Wilmoth. (2019) The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation. BMC Genomics 20(1): 254. • T. Zhebentyayeva, V. Shankar, R. Scorza, A. Callahan, M. Ravelonandro, S. Castro, T. Dejong, C. Saski and C. Dardick. (2019) Genetic characterization of world-wide Prunus domestica (plum) germplasm using sequence-based genotyping. Horticulture Research 6(1): 12. PMC6312543 • Y. Qiu, J. E. Milanes, J. A. Jones, R. E. Noorai, V. Shankar, and J. Morris. (2018) Glucose signalling is important for nutrient adaptation during differentiation of pleomorphic African trypanosomes. mSphere 3(5), e00366-18. PMC6211221. • A. Ramos-Garcia, V. Shankar, C. Saski, T. Hsiang and D. Freedman. (2018) Draft Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Pseudonocardia dioxanivorans BERK-1. Genome Announc 6(14), e00207-18. PMC5887028 • V. Shankar, R. Agans, and O. Paliy. (2017) Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities. Sci Rep 7(1): 6481. PMC5526943 • V. Shankar, M. Gouda, J. Moncivaiz, A. Gordon, N. V. Reo, L. Hussein, and O. Paliy. (2017) Differences in gut metabolites and microbial composition and functions between Egyptian and US teenagers are consistent with consumed diets. mSystems 2(1): e00169-16. PMC5296411 • O. Paliy and V. Shankar. (2016) Application of multivariate statistical techniques in microbial ecology. Mol. Ecol. 25(5), 1032-57. PMC4769650 • V. Shankar, N. Reo, and O. Paliy. (2015) Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome. Microbiome 3:73. PMC4675077. • V. Shankar, D. Homer, L. Rigsbee, H. J. Khamis, S. Michail, M. Raymer, N. V. Reo, and O. Paliy. (2015) The networks of human gut microbe-metabolite associations are different between health and irritable bowel syndrome. ISME J 9(8), 1899-903. PMID25635640. • V. Shankar, M. J. Hamilton, A. Khoruts, A. Kilburn, T. Unno, O. Paliy, and M. J. Sadowsky. (2014) Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation. Microbiome 2:13. PMC4030581. VIJAY SHANKAR CURRICULUM VITAE

• V. Shankar, R. Agans, B. Holmes, M. Raymer, and O. Paliy. (2013) Do gut microbial communities differ in pediatric IBS and health? Gut Microbes 4(4): 347-352. PMID23674073. • L. Rigsbee, R. Agans, V. Shankar, H. Kenche, H. Khamis, S. Michail, and O. Paliy. (2012) Quantitative profiling of gut microbiota of children with diarrhea-predominant Irritable Bowel Syndrome. Am. J. Gastroenterol. 107(11), 1740-51. PMID22986438.

BOOK CHAPTERS

• O. Paliy, V. Shankar, and M. Sagova-Mareckova. (2014). Chapter 9: Phylogenetic Microarrays. Bioinformatics and Data Analysis in Microbiology. Ed. Ozlem Tastan Bishop. Horizon/Caister press. 207-229. Print. • O. Paliy, V. Shankar. (2014). Chapter 11: Applications of Phylogenetic Microarrays in Profiling of Human Microbiomes. Microarrays: Current Technology, Innovation and Applications. Ed Melanie Woodward. Horizon press. 195-215. Print.

PRESENTATIONS

• V. Shankar, D. Homer, L. Rigsbee, H. Khamis, S. Michail, M. Raymer, N. Reo and O. Paliy. Fecal metabolites in pediatric IBS. American Society of Microbiology, National Conference, Washington DC, 2014. • V. Shankar, D. Homer, L. Rigsbee, H. Khamis, S. Michail, M. Raymer, N. Reo and O. Paliy. Fecal metabolites in pediatric IBS. Ohio Branch American Society of Microbiology, Ohio State University, OH, 2014. Won the award for the best graduate student poster presentation. • V. Shankar, L. Rigsbee, H. Kenche, S. Michail, and O. Paliy. Effects of VSL#3 on the composition of intestinal microbiota in IBS-D patients. FASEB Probiotics, Intestinal Microbiota and the Host, Carefree, AZ, 2011.

SKILLS

• Highly skilled in the use multivariate statistical and mathematical approaches to draw biological inferences from complex datasets (main focus of my doctoral dissertation). Also skilled in application of integrative approaches across multiple datasets to extract biological insights at the systems level (Systems Biology). • Expertise in the use of Next-Generation Sequencing technologies such as Illumina MiSeq, Ion Torrent PGM and Proton, and 454 Pyrosequencing to profile complex microbial communities. • Proficient at analyzing data acquired from Next-Generation Sequencing technologies and microarrays, and in building analysis pipelines for such datasets. • Highly skilled at analyzing and interpreting single cell transcriptomics data. • Proficiency in Matlab, Python and R scripting languages, and in UNIX environment. • Experienced in laboratory molecular biological techniques such as PCR, RT-PCR, qPCR, Nucleic Acid extraction and in molecular techniques required for NGS library prep and sequencing (Illumina and Life Technologies based). • Proficient as Systems Admin for HPC maintenance and in most operating systems and office related softwares. Also proficient in designing and building analysis workstations (hardware expertise).